pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Rafael,

There is a lot of info on the wiki:

   http://www.pymolwiki.org

also, there is a help system in pymol (type "help"). The run command
is what you want for running scripts.

gilleain torrance

On 2/27/07, Rafael Fern=E1ndez Leiro <le...@gm...> wrote:
> Hello, firstly excuse my english. I'll try to get understood.
>
> I have just arrived to  MacPyMol and I'm playing around with the
> program. I can't run any script. Is there anywhere a tutorial about
> how to setup MacPyMol to run scripts and how to use them? Thanks a lot.
>
> (I'm running MacPymolX11Hybrid of course)
>
> -------------------------------------------------------------------------
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Hello,

Has anyone explored the idea of other types of clipping shapes?  The current
clipping planes are parallel to the display.  What about an octant type 
clipping?  Or perhaps a clipping box?  

--Kevin


-- 
Kevin Neff
Mayo College of Medicine
Registered Linux User #432952

Hi there...

If you want to generate your morph-pdbs with sensible geometry, try this
script:
http://www.molmovdb.org/molmovdb/morph/download/morph_dist.inp

It requires CNS, but if you have start and end, it interpolates smoothly,
using all atoms, without distorting geometry of side chains and so on.

Can give very nice results, and is fully compatible with pymol.

D

On 28/02/07, Clara Marco <cm...@ib...> wrote:
>
> Hi!
> I'm trying to build a morphing movie to show the transition between
> two conformational states of a protein. I've run morphing with
> program LSQMAN, which has generated intermediate pdb files between
> start.pdb and end.pdb.The problem is that to avoid geometry
> distortions I've used a LSQMAN option that only uses CA's and few
> side chains (selected by proximity of the ligand that induces the
> conformational change), and now, the intermediate pdbs only have CA's
> coordinates.
> Is there any possibility to represent these pdb's with pymol
> (cartoon/ribbon)? I've tried it but it only represents points/spheres
> corresponding to the CA's.
> If not, does anyone know how to calculate morphing intermediate pdb's
> suitable to be represented with pymol?
> Thank you very much.
> Clara
> Clara Marco-Marin
> Instituto de Biomedicina de Valencia
> Consejo Superior de Investigaciones Cientificas
> C/Jaime Roig, 11
> 46010 Valencia
> Espa=F1a
>
>
> -------------------------------------------------------------------------
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--=20
---------------------------------------
David Briggs, PhD.
Father & Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile

Hi Clara

Try=20

set ribbon_trace_atoms, 1

or=20

set cartoon_trace_atoms, 1

Daniel

On Wed, 2007-02-28 at 10:10 +0100, Clara Marco wrote:
> Hi!
> I'm trying to build a morphing movie to show the transition between
> two conformational states of a protein. I've run morphing with
> program LSQMAN, which has generated intermediate pdb files between
> start.pdb and end.pdb.The problem is that to avoid geometry
> distortions I've used a LSQMAN option that only uses CA's and few
> side chains (selected by proximity of the ligand that induces the
> conformational change), and now, the intermediate pdbs only have CA's
> coordinates.
> Is there any possibility to represent these pdb's with pymol
> (cartoon/ribbon)? I've tried it but it only represents points/spheres
> corresponding to the CA's.
> If not, does anyone know how to calculate morphing intermediate pdb's
> suitable to be represented with pymol?
> Thank you very much.
> Clara=20
> Clara Marco-Marin
> Instituto de Biomedicina de Valencia
> Consejo Superior de Investigaciones Cientificas
> C/Jaime Roig, 11
> 46010 Valencia
> Espa=C3=B1a
>=20
>=20
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share y=
our
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--=20
Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.

Hi!
I'm trying to build a morphing movie to show the transition between
two conformational states of a protein=2E I've run morphing with
program LSQMAN, which has generated intermediate pdb files between
start=2Epdb and end=2Epdb=2EThe problem is that to avoid geometry
distortions I've used a LSQMAN option that only uses CA's and few
side chains (selected by proximity of the ligand that induces the
conformational change), and now, the intermediate pdbs only have CA's
coordinates=2E
Is there any possibility to represent these pdb's with pymol
(cartoon/ribbon)=3F I've tried it but it only represents points/spheres
corresponding to the CA's=2E
If not, does anyone know how to calculate morphing intermediate pdb's
suitable to be represented with pymol=3F
Thank you very much=2E
Clara=20
Clara Marco-Marin
Instituto de Biomedicina de Valencia
Consejo Superior de Investigaciones Cientificas
C/Jaime Roig, 11
46010 Valencia
Espa=F1a

Hello, firstly excuse my english. I'll try to get understood.

I have just arrived to  MacPyMol and I'm playing around with the  
program. I can't run any script. Is there anywhere a tutorial about  
how to setup MacPyMol to run scripts and how to use them? Thanks a lot.

(I'm running MacPymolX11Hybrid of course)

wizard box

(choose plane)
(click auto-position 99%)
(use mouse to rotate)
(toggle points)
(use scroll wheel to increase clipping slab width)

ray

 
--
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Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 
________________________________

	From: pym...@li...
[mailto:pym...@li...] On Behalf Of David Briggs
	Sent: Tuesday, February 27, 2007 5:05 AM
	To: pym...@li...
	Subject: [PyMOL] Projecting shadows onto a background.
	
	
	Hi Pymol-ers.
	
	Does anyone know how I can use pymol to project a shadow of my
protein onto a background?
	
	Cheers,
	
	Dave
	
	-- 
	---------------------------------------
	David Briggs, PhD. 
	Father & Crystallographer
	www.dbriggs.talktalk.net
	iChat AIM ID: DBassophile 

Hi Pymol-ers.

Does anyone know how I can use pymol to project a shadow of my protein onto
a background?

Cheers,

Dave

-- 
---------------------------------------
David Briggs, PhD.
Father & Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile

Hi,

I have PyMOL-0.99rc6 in SuSE Pro 9.3. I have a script that generates
labels in the screen. At the end I generate a PNG output. All of this
works when I use PyMOL interactively. The output PNG file is fine.

But when I run PyMOL in batch mode (-c flag), the PNG file created does
not show the labels. Has anyone seen this before? Is this the way it is
supposed to work?

Thanks,
Prakash

Does anyone know of the best way to get a scene export of all polygons
currently being used? I am not afraid to modify the pymol source and
have done so for other custom projects. The vrml export option is very
much appreciated but exporting stick models has the unfortunate
consequence that the bonds are exported as cylinders as opposed to
polygons, which results in the vrml interpreter rendering the sticks
with lots of polygons.

Has anyone looked into solutions for this problem other than getting
your vrml importer to use more coarse primitives?

Aaron

I found an old version of my code.  It was just slightly more
complicated than I thought.  Here's a version of the wrapper that I
was using:

import sys

sys.path.append('/home/mlerner/work/src/PyMOL_Plugins/')

import SomethingOrOtherTools
def __init__(self):
    self.menuBar.addmenuitem('Plugin', 'command',
                             'SomethingOrOther',
                             label='SomethingOrOther...',
                             command = lambda s=self:
getSomethingOrOtherTools(s))

def getSomethingOrOtherTools(thing):
    reload(SomethingOrOtherTools)
    return SomethingOrOtherTools.SomethingOrOtherTools(thing)


Let me know if you have any more questions.

-michael

On 2/24/07, Michael Lerner <mgl...@gm...> wrote:
> Actually, I did this when I was developing the APBS Plugin.  I put all
> of the interesting code in a module called _apbs_tools.  apbs_tools
> was just a little wrapper where the init function would import and
> reload _apbs_tools and then call through to it.
>
> -Michael
>
> On 2/24/07, DeLano Scientific <de...@de...> wrote:
> > I believe this is a limitation of Python:  once a code module is loaded and
> > initialized, it is difficult to reload it...you might be able to hack it
> > though.
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On Behalf
> > > Of bgbg bg
> > > Sent: Saturday, February 24, 2007 5:19 AM
> > > To: pym...@li...
> > > Subject: [PyMOL] reload modified wizard
> > >
> > > Hello,
> > > I develop several custom PyMol wizards. Is there any way to
> > > reload a modified wizard,  without restarting PyMol?
> > >
> > > Thank you.
> > >
> > > --------------------------------------------------------------
> > > -----------
> > > Take Surveys. Earn Cash. Influence the Future of IT Join
> > > SourceForge.net's Techsay panel and you'll get the chance to
> > > share your opinions on IT & business topics through brief
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> > > &CID=DEVDEV
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> > -------------------------------------------------------------------------
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> >
>
>
> --
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner http://lernerclan.net
>


-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net

Continuing my thread 'reloading wizards' (started on Feb 24).
Sometimes, in my pml scripts, I want to produce 'command buttons' like
those obtained by get_panel( .. ) function that is present in all the
wizards. The functionality of those scripts do not justify converting
them to built-in wizards. My guess that it is possible to make a
wizard ('load_panel_commands) that will read a text file with all the
needed parameters and then call get_panel accordingly. Is there a
better/easier way to obtain this kind of functionality?

Actually, I did this when I was developing the APBS Plugin.  I put all
of the interesting code in a module called _apbs_tools.  apbs_tools
was just a little wrapper where the init function would import and
reload _apbs_tools and then call through to it.

-Michael

On 2/24/07, DeLano Scientific <de...@de...> wrote:
> I believe this is a limitation of Python:  once a code module is loaded and
> initialized, it is difficult to reload it...you might be able to hack it
> though.
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf
> > Of bgbg bg
> > Sent: Saturday, February 24, 2007 5:19 AM
> > To: pym...@li...
> > Subject: [PyMOL] reload modified wizard
> >
> > Hello,
> > I develop several custom PyMol wizards. Is there any way to
> > reload a modified wizard,  without restarting PyMol?
> >
> > Thank you.
> >
> > --------------------------------------------------------------
> > -----------
> > Take Surveys. Earn Cash. Influence the Future of IT Join
> > SourceForge.net's Techsay panel and you'll get the chance to
> > share your opinions on IT & business topics through brief
> > surveys-and earn cash
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> > &CID=DEVDEV
> > _______________________________________________
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> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> -------------------------------------------------------------------------
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>


-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net

I believe this is a limitation of Python:  once a code module is loaded and
initialized, it is difficult to reload it...you might be able to hack it
though.

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of bgbg bg
> Sent: Saturday, February 24, 2007 5:19 AM
> To: pym...@li...
> Subject: [PyMOL] reload modified wizard
> 
> Hello,
> I develop several custom PyMol wizards. Is there any way to 
> reload a modified wizard,  without restarting PyMol?
> 
> Thank you.
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
> surveys-and earn cash 
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> &CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

This problem is usually caused by running out of colors used to encode atoms
during interactive selection -- that can happen when the display is in
16-bit (thousands of colors) as opposed to 24/32-bit (millions of colors).


Please double-check the Display settings in System Preferences.

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of bgbg bg
> Sent: Saturday, February 24, 2007 2:23 AM
> To: Heidi Privett
> Cc: pym...@li...
> Subject: Re: [PyMOL] trouble selecting residues with mouse
> 
> I also have such a problem (on Linux). Couldn't find any 
> solution though.
> 
> On 2/8/07, Heidi Privett <pr...@ca...> wrote:
> > I have been trying to run the latest version of MacPyMOL on my new 
> > iMac with an Intel Core 2 Duo processor and the latest 
> version of OSX.  
> > I have noticed problems trying to select residues with my mouse 
> > (either control-clicking to select or double clicking to get the 
> > menu).  I can select some residues normally, but for others, when I 
> > control-click on them, a residue in another part of the 
> protein gets selected.  Still other residues cannot be selected
> > at all using the mouse.   This also happens with I try to 
> pick atoms with
> > the mouse.
> >
> > I've seen this happen with multiple PDB files and older 
> versions of MacPyMOL
> > as well.    I don't have any problems selecting residues or 
> atoms with the
> > command line.
> >
> > This problem seems to be similar to the one that someone was having 
> > with the
> > X11 version a couple of weeks ago.  Does anyone have any 
> suggestions?
> >
> > Thanks.
> > Heidi
> >
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Heidi K. Privett
> > Graduate Student
> > Division of Chemistry and Chemical Engineering California 
> Institute of 
> > Technology 1200 E. California Blvd.  MC 114-96 Pasadena, CA 
> 91125 USA
> >
> > pr...@ca...
> >
> >
> >
> >
> > 
> ----------------------------------------------------------------------
> > --- Using Tomcat but need to do more? Need to support web services, 
> > security?
> > Get stuff done quickly with pre-integrated technology to 
> make your job 
> > easier.
> > Download IBM WebSphere Application Server v.1.0.1 based on Apache 
> > Geronimo
> > 
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216
> > 42 _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> 
> --------------------------------------------------------------
> -----------
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> SourceForge.net's Techsay panel and you'll get the chance to 
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Hello,
I develop several custom PyMol wizards. Is there any way to reload a
modified wizard,  without restarting PyMol?

Thank you.

I also have such a problem (on Linux). Couldn't find any solution though.

On 2/8/07, Heidi Privett <pr...@ca...> wrote:
> I have been trying to run the latest version of MacPyMOL on my new iMac with
> an Intel Core 2 Duo processor and the latest version of OSX.  I have noticed
> problems trying to select residues with my mouse (either control-clicking to
> select or double clicking to get the menu).  I can select some residues
> normally, but for others, when I control-click on them, a residue in another
> part of the protein gets selected.  Still other residues cannot be selected
> at all using the mouse.   This also happens with I try to pick atoms with
> the mouse.
>
> I've seen this happen with multiple PDB files and older versions of MacPyMOL
> as well.    I don't have any problems selecting residues or atoms with the
> command line.
>
> This problem seems to be similar to the one that someone was having with the
> X11 version a couple of weeks ago.  Does anyone have any suggestions?
>
> Thanks.
> Heidi
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Heidi K. Privett
> Graduate Student
> Division of Chemistry and Chemical Engineering
> California Institute of Technology
> 1200 E. California Blvd.  MC 114-96
> Pasadena, CA 91125 USA
>
> pr...@ca...
>
>
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier.
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

Anthony,

In the latest 1.0 beta open-source code and builds, you'll find a
label_digits setting that can control the number of digits after the decimal
place.  The new default is one digit.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of gilleain torrance
> Sent: Friday, February 23, 2007 2:16 PM
> To: pym...@li...
> Subject: Re: [PyMOL] Distance Label Format
> 
> Hi,
> 
> Hmm. Not very easily. The measurement wizard just calls a 
> distance method, which makes the dashed line and the label 
> internally. Other wise it would be simple to say:
> 
>   cmd.label_dash("%0.1f" % d)
> 
> assuming that there was such a command... :) Oh, and that 
> command would need a dash object as a parameter.
> 
> So, no, not that I can see.
> 
> gilleain torrance
> 
> On 2/23/07, Anthony Armstrong <arm...@qu...> wrote:
> > Hi Folks,
> >
> > When using the distance wizard is there a way to change the 
> number of 
> > decimal places output to the label from 2 to 1?
> >
> > Thanks,
> > Tony
> >
> > Anthony A. Armstrong
> > Department of Biophysics and Biophysical Chemistry Johns Hopkins 
> > University School of Medicine
> > 725 North Wolfe Street
> > Baltimore, MD 21205
> > 410-955-8715
> > 410-955-0637 FAX
> > arm...@gr...
> >
> > 
> ----------------------------------------------------------------------
> > --- Take Surveys. Earn Cash. Influence the Future of IT Join 
> > SourceForge.net's Techsay panel and you'll get the chance to share 
> > your opinions on IT & business topics through brief 
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> > cash 
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> > DEV _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
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Hi,

Hmm. Not very easily. The measurement wizard just calls a distance
method, which makes the dashed line and the label internally. Other
wise it would be simple to say:

  cmd.label_dash("%0.1f" % d)

assuming that there was such a command... :) Oh, and that command
would need a dash object as a parameter.

So, no, not that I can see.

gilleain torrance

On 2/23/07, Anthony Armstrong <arm...@qu...> wrote:
> Hi Folks,
>
> When using the distance wizard is there a way to change the number of
> decimal places output to the label from 2 to 1?
>
> Thanks,
> Tony
>
> Anthony A. Armstrong
> Department of Biophysics and Biophysical Chemistry
> Johns Hopkins University School of Medicine
> 725 North Wolfe Street
> Baltimore, MD 21205
> 410-955-8715
> 410-955-0637 FAX
> arm...@gr...
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Hi Folks,

When using the distance wizard is there a way to change the number of
decimal places output to the label from 2 to 1?

Thanks,
Tony

Anthony A. Armstrong
Department of Biophysics and Biophysical Chemistry
Johns Hopkins University School of Medicine
725 North Wolfe Street
Baltimore, MD 21205
410-955-8715
410-955-0637 FAX
arm...@gr...

Dear Bernhard,

The user manual is quite informative where it comes to making
selections. There is not a polar/nonpolar grouping made for you, but
you can easily select the residues based on their names (resn or r.).

select basic, (resn lys,his,arg)

As a side note, on this as well as all other user lists, it is
preferred that you set a subject line which reflects the question
you're asking. Since many of us are dedicating our own time to
answering, we usually make a preselection of the mails we could
possibly provide an answer to. Mails without subject are likely to be
thrown away unread.

Cheers,

Tsjerk


On 2/23/07, Bernhard Kleine <bb...@gm...> wrote:
> Hello and good morning,
>
> being newly arrived in this list, I am a molecular biologist working
> recently in endocrinology and epigenetics and living in the black forest
> in the south west of germany.
>
> Since I am not fully content with the picture quality which I can get
> with Rasmol, I am trying to use PyMOL. However, since I try to adopt my
> rasmol script for use in PyMOL, I am unable to find how to select
> individual amino acids, or e.g. polar or basic residues. I am quite
> convinced that such shortcuts exist. But either the refmanual oder the
> usermanual lack mentioning any typ of aminoacids, so far as I can say
> (searching with Acrobat reader).
>
> It would be a pleasure if anyone could point me to the proper
> information.
>
> Thanks a lot
>
> Bernhard
> --
> Bernhard Kleine
> mail bb...@gm...
> linux-user Nr. 411598
> ****************************************
> PGP-Key         PGP-Fingerprint:
> 0x6C1D9C2A      3161 A9E2 B661 A242 D9AF
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hello and good morning,

being newly arrived in this list, I am a molecular biologist working
recently in endocrinology and epigenetics and living in the black forest
in the south west of germany.

Since I am not fully content with the picture quality which I can get
with Rasmol, I am trying to use PyMOL. However, since I try to adopt my
rasmol script for use in PyMOL, I am unable to find how to select
individual amino acids, or e.g. polar or basic residues. I am quite
convinced that such shortcuts exist. But either the refmanual oder the
usermanual lack mentioning any typ of aminoacids, so far as I can say
(searching with Acrobat reader).

It would be a pleasure if anyone could point me to the proper
information.

Thanks a lot

Bernhard
--=20
Bernhard Kleine
mail bb...@gm...
linux-user Nr. 411598
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Michael,

This is definitely going to happen -- having seen how the slider works in
pro-animation tools in Cinema4D, I am convinced that the equivalent
capability would be extremely useful in PyMOL, not just for MD, but for
working with animated movies comprised of multiple scenes.

However, it clashes a bit with the "mdo" movie command paradigm, since that
assumes forward sequention actions rather than random access.  The "mview"
approach has solved that issue with respect to camera and object matrixes
(and soon with scenes too), so really, it is just a matter of my finding the
development time to make this happen.  For reasons of internal performance,
my solution will be integrated into the main OpenGL GUI as opposed to being
external.  

However, the ability to randomly jump to a particular movie frame while
maintaining movie coherence will be exposed as an API function enabling
similar functionality to be developedas a plugin, such as an MD-specific
browsing interface.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 
"Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@de... to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor!" -WLD
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Michael Lerner
> Sent: Thursday, February 22, 2007 12:16 PM
> To: pym...@li...
> Subject: [PyMOL] Slider for movies?
> 
> Hi,
> 
> I'm using PyMOL to look at Amber trajectories.  It would be 
> really useful if I could zoom around the movie with a slider, 
> like in VMD.
> Has anybody seen (or written) a plugin to do such a thing?
> 
> It would also be nice if I could say "each frame is 5ps and 
> the movie starts at time=500ps" and have the slider display 
> things accordingly, but I figure that's a little more of a long shot.
> 
> Thank you,
> 
> -michael
> 
> --
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner http://lernerclan.net
> 
> --------------------------------------------------------------
> -----------
> Take Surveys. Earn Cash. Influence the Future of IT Join 
> SourceForge.net's Techsay panel and you'll get the chance to 
> share your opinions on IT & business topics through brief 
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&CID=DEVDEV
> _______________________________________________
> PyMOL-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,

I'm using PyMOL to look at Amber trajectories.  It would be really
useful if I could zoom around the movie with a slider, like in VMD.
Has anybody seen (or written) a plugin to do such a thing?

It would also be nice if I could say "each frame is 5ps and the movie
starts at time=500ps" and have the slider display things accordingly,
but I figure that's a little more of a long shot.

Thank you,

-michael

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net

Hello,

I've developped a plugin that add the possibility to use Open Babel. This 
permits you to import all file formats supported by Open Babel. This plugin 
use the Python wrapper of Open Babel.

You can get it here:
http://sourceforge.net/project/showfiles.php?group_id=189996&package_id=222732

Cheers,

Jerome Pansanel